6HTF | pdb_00006htf

Crystal structure of human Btk SH2 domain bound to rF10 repebody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.256 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6HTF

This is version 1.2 of the entry. See complete history

Literature

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms.

Duarte, D.P.Lamontanara, A.J.La Sala, G.Jeong, S.Sohn, Y.K.Panjkovich, A.Georgeon, S.Kukenshoner, T.Marcaida, M.J.Pojer, F.De Vivo, M.Svergun, D.Kim, H.S.Dal Peraro, M.Hantschel, O.

(2020) Nat Commun 11: 2319-2319

  • DOI: https://doi.org/10.1038/s41467-020-16128-5
  • Primary Citation Related Structures: 
    6HTF

  • PubMed Abstract: 

    Bruton's tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition.


  • Organizational Affiliation
    • Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL, 1015, Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 44.35 kDa 
  • Atom Count: 3,041 
  • Modeled Residue Count: 362 
  • Deposited Residue Count: 391 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK117Homo sapiensMutation(s): 0 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
GTEx:  ENSG00000010671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
rF10 repebody274synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.256 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.521α = 90
b = 32.947β = 90
c = 80.624γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
SwitzerlandKLS_3595_02_2015
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary